Real-time analysis of RAG complex activity in V(D)J recombination

Significance Recombination-activating genes 1 and 2 (RAG1/2) and high mobility group box 1 (HMGB1) create dsDNA breaks at recombination signal sequences (RSSs), initiating the variable, diversity, and joining [V(D)J] recombination pathway for antigen–receptor gene assembly. We have discovered that RAG complex binds and bends RSS DNA at the heptamer, with different binding modes for 12RSS and 23RSS substrates. Our experimentally derived binding kinetics have established that binding, bending, and synapsis precede catalysis. We have also directly observed the dynamics of the synaptic complex, revealing that RAG1/2 bending places the nonamers at nearly perpendicular orientations and that the RAG:12RSS:23RSS synaptic complex is very stable. We provide a kinetic model that integrates physical binding, bending, and synapsis steps of the RAG1/2 pathway.